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Are you connecting it so that you can control the output and read the salt from your indoor panel? I don't usually recommend this installation as it tends to control your chlorine levels better when it's not connected to be controlled by the Intellitouch. You will loose the Automatic Temperature Compensation and the Salt Amount Feature. In addition, when there are sevice lights, the AP will not show the display as to why it's flashing. You can, however, DISABLE REMOTE, to monitor and diagnose the AP directly on the Digital unit.

However, to connect the two, you need to connect the following:
AP Red to Pentair Red
AP Black to Pentair Yellow
AP Yellow to Pentair Green
AP Green to Pentair Black.

That error message sounds like "Error! Purifier off Check Flow", which usually means the trisensor is not seeing sufficent water flow through the manifold or the trisensor cable is not connected properly.

Sean,
Depending on your model, there may be an option for you to SELECT REMOTE. This should be set on "2" (factory setting is "1").
The 1 is for a Jandy control system. 2 is for Pentaire and Polaris.

The Intellitouch should allow you to control the Purifier %, Boost cycles, salt, and when there is a warning condition.

Let me know if that does it.

I realized I did not answer your question regarding the 3 holes on the cell cord, and the 2 prongs on your SC-48 cell, which I'm sure by now you've come to figure it out. It doesn't matter which two holes you use. The center hole will be connected/uesd in either case, and the two outer holes are spliced together back at the power supply anyway.

Sorry fot the delay in response. I will check into that. Actually, my recommendation would be to not interface the two because you lose the Automatic Temperature Compensation feature and the Salt Amount display.

Well Sean,
I'm going back to my inital response of running the Pool Pilot as a separate component and not interfaced to the Intellitouch!
After describing the problem with the Pentair tech guy, I got "We only support the intellichlor". When I asked if there was a software change because we use to communicate fine, he said there were none the he knew of....so again I said everything esle seems to be ok except the salt display is showing 0 ppm. "We only support the intellichlor".
I can check with my engineering dept to see if there's a solution, but at this point, again, disconnected the interface wires and run the Pool Pilot separately. It sholdn't take you but a week or two to get the correct setting on the Pool Pilot to maintain your pool.